| 5_blade 5FLW_A |
| ID: | 1483622789 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 302 (289) | ||
| Sequences: | 2558 (1557.9) | ||
| Seq/Len: | 8.851 | ||
| Nf(neff/√len): | 91.6 |
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: 8.851).
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 |
| 53_D | 56_A | 6.435 | 1.00 |
| 146_S | 162_R | 5.988 | 1.00 |
| 29_T | 50_T | 5.016 | 1.00 |
| 29_T | 52_T | 4.178 | 1.00 |
| 197_L | 219_T | 4.158 | 1.00 |
| 197_L | 217_T | 3.850 | 1.00 |
| 33_Y | 121_F | 3.731 | 1.00 |
| 92_K | 113_V | 3.679 | 1.00 |
| 92_K | 115_D | 3.586 | 1.00 |
| 162_R | 171_V | 3.244 | 1.00 |
| 164_A | 169_T | 2.582 | 1.00 |
| 26_F | 93_Y | 2.534 | 1.00 |
| 217_T | 226_S | 2.323 | 1.00 |
| 284_A | 287_V | 2.293 | 1.00 |
| 113_V | 124_Q | 2.271 | 1.00 |
| 63_V | 95_M | 2.213 | 1.00 |
| 50_T | 60_H | 2.152 | 1.00 |
| 25_K | 28_D | 2.127 | 1.00 |
| 218_A | 224_P | 2.125 | 1.00 |
| 164_A | 171_V | 2.074 | 1.00 |
| 141_Q | 147_G | 2.070 | 1.00 |
| 143_E | 193_K | 2.068 | 1.00 |
| 193_K | 198_Y | 1.998 | 1.00 |
| 137_I | 149_I | 1.944 | 1.00 |
| 84_V | 95_M | 1.937 | 1.00 |
| 219_T | 226_S | 1.900 | 1.00 |
| 86_H | 91_G | 1.899 | 1.00 |
| 51_T | 57_W | 1.838 | 1.00 |
| 33_Y | 117_P | 1.815 | 1.00 |
| 248_P | 257_E | 1.804 | 1.00 |
| 100_E | 107_A | 1.799 | 1.00 |
| 33_Y | 84_V | 1.799 | 1.00 |
| 150_M | 200_W | 1.709 | 1.00 |
| 256_S | 280_P | 1.676 | 1.00 |
| 117_P | 121_F | 1.634 | 1.00 |
| 150_M | 160_I | 1.629 | 1.00 |
| 249_L | 256_S | 1.598 | 1.00 |
| 87_C | 90_T | 1.596 | 1.00 |
| 51_T | 54_F | 1.595 | 1.00 |
| 198_Y | 221_L | 1.590 | 1.00 |
| 271_L | 274_S | 1.582 | 1.00 |
| 88_P | 141_Q | 1.528 | 1.00 |
| 140_F | 198_Y | 1.493 | 1.00 |
| 277_V | 280_P | 1.488 | 1.00 |
| 50_T | 118_T | 1.481 | 1.00 |
| 165_D | 168_L | 1.481 | 1.00 |
| 114_A | 120_P | 1.481 | 1.00 |
| 283_I | 288_A | 1.449 | 0.99 |
| 160_I | 222_H | 1.432 | 0.99 |
| 109_I | 149_I | 1.431 | 0.99 |
| 164_A | 168_L | 1.429 | 0.99 |
| 186_L | 202_G | 1.422 | 0.99 |
| 48_C | 84_V | 1.420 | 0.99 |
| 94_V | 111_V | 1.419 | 0.99 |
| 153_D | 157_G | 1.410 | 0.99 |
| 116_A | 120_P | 1.404 | 0.99 |
| 166_D | 169_T | 1.400 | 0.99 |
| 113_V | 122_A | 1.394 | 0.99 |
| 45_G | 62_I | 1.391 | 0.99 |
| 124_Q | 168_L | 1.379 | 0.99 |
| 90_T | 147_G | 1.375 | 0.99 |
| 25_K | 250_D | 1.369 | 0.99 |
| 218_A | 221_L | 1.369 | 0.99 |
| 192_I | 246_V | 1.328 | 0.99 |
| 161_Y | 170_I | 1.328 | 0.99 |
| 165_D | 169_T | 1.320 | 0.99 |
| 83_K | 138_G | 1.320 | 0.99 |
| 206_T | 211_N | 1.314 | 0.99 |
| 24_Q | 93_Y | 1.300 | 0.99 |
| 20_G | 35_E | 1.297 | 0.99 |
| 81_R | 243_V | 1.274 | 0.98 |
| 114_A | 119_G | 1.264 | 0.98 |
| 191_I | 221_L | 1.261 | 0.98 |
| 116_A | 121_F | 1.254 | 0.98 |
| 47_C | 59_S | 1.253 | 0.98 |
| 96_Y | 111_V | 1.248 | 0.98 |
| 36_N | 47_C | 1.244 | 0.98 |
| 34_G | 49_Y | 1.238 | 0.98 |
| 218_A | 223_G | 1.238 | 0.98 |
| 116_A | 119_G | 1.232 | 0.98 |
| 33_Y | 46_V | 1.212 | 0.98 |
| 33_Y | 63_V | 1.212 | 0.98 |
| 51_T | 56_A | 1.205 | 0.97 |
| 138_G | 150_M | 1.183 | 0.97 |
| 53_D | 57_W | 1.182 | 0.97 |
| 138_G | 158_T | 1.161 | 0.97 |
| 152_E | 159_H | 1.152 | 0.96 |
| 125_T | 169_T | 1.138 | 0.96 |
| 147_G | 163_L | 1.138 | 0.96 |
| 47_C | 62_I | 1.138 | 0.96 |
| 293_S | 297_E | 1.132 | 0.96 |
| 33_Y | 48_C | 1.129 | 0.96 |
| 21_I | 32_A | 1.119 | 0.96 |
| 61_G | 118_T | 1.109 | 0.95 |
| 78_I | 100_E | 1.101 | 0.95 |
| 217_T | 287_V | 1.091 | 0.95 |
| 98_H | 107_A | 1.086 | 0.94 |
| 22_G | 190_T | 1.082 | 0.94 |
| 10_D | 14_D | 1.078 | 0.94 |
| 158_T | 189_P | 1.072 | 0.94 |
| 284_A | 289_S | 1.065 | 0.94 |
| 214_K | 230_L | 1.062 | 0.94 |
| 109_I | 137_I | 1.057 | 0.93 |
| 28_D | 52_T | 1.054 | 0.93 |
| 26_F | 86_H | 1.053 | 0.93 |
| 48_C | 63_V | 1.053 | 0.93 |
| 115_D | 122_A | 1.044 | 0.93 |
| 258_H | 277_V | 1.042 | 0.93 |
| 78_I | 104_Y | 1.041 | 0.93 |
| 95_M | 112_A | 1.039 | 0.93 |
| 64_L | 112_A | 1.038 | 0.93 |
| 80_E | 98_H | 1.034 | 0.92 |
| 140_F | 191_I | 1.034 | 0.92 |
| 9_H | 12_S | 1.026 | 0.92 |
| 30_W | 51_T | 1.024 | 0.92 |
| 259_F | 281_I | 1.019 | 0.92 |
| 23_L | 30_W | 1.008 | 0.91 |
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 | |
| 3vsfA | 6 | 0.9702 | 100 | 0.264 | Contact Map |
| 3nqhA | 1 | 0.9669 | 100 | 0.289 | Contact Map |
| 2exhA | 4 | 0.9238 | 100 | 0.358 | Contact Map |
| 3c2uA | 4 | 0.9272 | 100 | 0.359 | Contact Map |
| 1yifA | 4 | 0.9238 | 100 | 0.365 | Contact Map |
| 1yrzA | 2 | 0.9238 | 100 | 0.367 | Contact Map |
| 1uv4A | 1 | 0.8841 | 100 | 0.39 | Contact Map |
| 3zxkA | 2 | 0.8874 | 100 | 0.395 | Contact Map |
| 4kc7A | 3 | 0.9073 | 100 | 0.406 | Contact Map |
| 3kstA | 2 | 0.9073 | 100 | 0.406 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)