| solo_1laf |
| ID: | 1402683850 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 235 (230) | ||
| Sequences: | 1140 (832.8) | ||
| Seq/Len: | 4.957 | ||
| Nf(neff/√len): | 54.9 |
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: 4.957).
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 |
| 34_E | 38_R | 3.463 | 1.00 |
| 113_G | 153_L | 3.132 | 1.00 |
| 34_E | 37_K | 3.042 | 1.00 |
| 36_C | 43_C | 2.891 | 1.00 |
| 56_S | 62_I | 2.826 | 1.00 |
| 148_L | 153_L | 2.600 | 1.00 |
| 79_I | 196_G | 2.464 | 1.00 |
| 73_D | 76_Q | 2.144 | 1.00 |
| 198_R | 201_D | 2.134 | 1.00 |
| 50_F | 53_L | 2.121 | 1.00 |
| 138_Y | 147_D | 2.086 | 1.00 |
| 71_I | 76_Q | 2.051 | 1.00 |
| 121_E | 125_N | 2.046 | 1.00 |
| 19_D | 23_E | 2.036 | 1.00 |
| 54_I | 79_I | 1.972 | 1.00 |
| 113_G | 148_L | 1.965 | 1.00 |
| 147_D | 152_R | 1.934 | 1.00 |
| 72_T | 75_R | 1.893 | 1.00 |
| 30_D | 33_N | 1.890 | 1.00 |
| 32_G | 45_W | 1.886 | 1.00 |
| 71_I | 194_G | 1.844 | 1.00 |
| 121_E | 137_A | 1.835 | 1.00 |
| 220_T | 223_K | 1.821 | 1.00 |
| 71_I | 84_K | 1.799 | 1.00 |
| 83_D | 209_D | 1.740 | 1.00 |
| 112_V | 155_A | 1.695 | 0.99 |
| 57_L | 65_I | 1.688 | 0.99 |
| 75_R | 81_F | 1.676 | 0.99 |
| 10_T | 16_S | 1.675 | 0.99 |
| 32_G | 43_C | 1.674 | 0.99 |
| 33_N | 45_W | 1.664 | 0.99 |
| 34_E | 215_L | 1.655 | 0.99 |
| 7_G | 62_I | 1.619 | 0.99 |
| 94_A | 98_S | 1.618 | 0.99 |
| 57_L | 69_L | 1.604 | 0.99 |
| 19_D | 25_I | 1.604 | 0.99 |
| 58_K | 78_E | 1.592 | 0.99 |
| 18_K | 47_A | 1.585 | 0.99 |
| 53_L | 62_I | 1.582 | 0.99 |
| 62_I | 65_I | 1.558 | 0.99 |
| 115_L | 118_S | 1.553 | 0.99 |
| 205_K | 209_D | 1.532 | 0.99 |
| 38_R | 218_D | 1.521 | 0.99 |
| 70_S | 75_R | 1.497 | 0.98 |
| 36_C | 39_M | 1.425 | 0.98 |
| 48_S | 53_L | 1.415 | 0.98 |
| 32_G | 39_M | 1.410 | 0.97 |
| 215_L | 221_Y | 1.409 | 0.97 |
| 65_I | 69_L | 1.385 | 0.97 |
| 29_I | 33_N | 1.376 | 0.97 |
| 32_G | 66_I | 1.360 | 0.97 |
| 48_S | 62_I | 1.342 | 0.96 |
| 222_D | 226_K | 1.330 | 0.96 |
| 74_K | 77_Q | 1.301 | 0.95 |
| 50_F | 69_L | 1.299 | 0.95 |
| 5_R | 46_V | 1.292 | 0.95 |
| 98_S | 101_Q | 1.289 | 0.95 |
| 197_L | 208_F | 1.286 | 0.95 |
| 24_F | 29_I | 1.280 | 0.95 |
| 35_M | 39_M | 1.278 | 0.95 |
| 50_F | 65_I | 1.261 | 0.94 |
| 48_S | 56_S | 1.257 | 0.94 |
| 52_A | 56_S | 1.224 | 0.93 |
| 49_D | 53_L | 1.222 | 0.93 |
| 28_D | 85_L | 1.218 | 0.93 |
| 225_A | 232_N | 1.214 | 0.93 |
| 111_H | 136_V | 1.208 | 0.92 |
| 70_S | 85_L | 1.208 | 0.92 |
| 17_S | 25_I | 1.196 | 0.92 |
| 9_D | 12_Y | 1.187 | 0.92 |
| 24_F | 47_A | 1.176 | 0.91 |
| 215_L | 218_D | 1.172 | 0.91 |
| 213_T | 217_Q | 1.160 | 0.90 |
| 15_F | 86_Y | 1.157 | 0.90 |
| 54_I | 69_L | 1.151 | 0.90 |
| 148_L | 156_A | 1.150 | 0.90 |
| 57_L | 62_I | 1.149 | 0.90 |
| 49_D | 52_A | 1.132 | 0.89 |
| 8_T | 29_I | 1.130 | 0.89 |
| 25_I | 30_D | 1.122 | 0.88 |
| 38_R | 214_E | 1.122 | 0.88 |
| 82_S | 85_L | 1.121 | 0.88 |
| 69_L | 79_I | 1.120 | 0.88 |
| 55_P | 79_I | 1.113 | 0.88 |
| 52_A | 55_P | 1.113 | 0.88 |
| 13_A | 17_S | 1.102 | 0.87 |
| 125_N | 137_A | 1.101 | 0.87 |
| 82_S | 208_F | 1.101 | 0.87 |
| 144_I | 156_A | 1.098 | 0.87 |
| 58_K | 79_I | 1.094 | 0.86 |
| 36_C | 41_V | 1.092 | 0.86 |
| 107_L | 110_K | 1.090 | 0.86 |
| 18_K | 24_F | 1.078 | 0.85 |
| 197_L | 205_K | 1.077 | 0.85 |
| 14_P | 17_S | 1.076 | 0.85 |
| 90_S | 120_Q | 1.071 | 0.85 |
| 129_R | 132_G | 1.069 | 0.85 |
| 9_D | 16_S | 1.068 | 0.85 |
| 32_G | 53_L | 1.062 | 0.84 |
| 222_D | 225_A | 1.058 | 0.84 |
| 26_G | 30_D | 1.053 | 0.83 |
| 53_L | 65_I | 1.047 | 0.83 |
| 32_G | 64_A | 1.029 | 0.82 |
| 33_N | 37_K | 1.018 | 0.81 |
| 38_R | 215_L | 1.012 | 0.80 |
| 5_R | 44_T | 1.008 | 0.80 |
| 50_F | 62_I | 1.003 | 0.79 |
| 9_D | 15_F | 1.002 | 0.79 |
| 8_T | 67_S | 1.001 | 0.79 |
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 | |
| 1wdnA | 1 | 0.9489 | 100 | 0.314 | Contact Map |
| 4oenA | 2 | 0.9404 | 100 | 0.333 | Contact Map |
| 1lstA | 1 | 1 | 100 | 0.374 | Contact Map |
| 2ylnA | 1 | 0.9532 | 100 | 0.393 | Contact Map |
| 1pb7A | 1 | 0.9234 | 100 | 0.403 | Contact Map |
| 4g4pA | 1 | 0.9447 | 100 | 0.407 | Contact Map |
| 3vv5A | 2 | 0.9489 | 100 | 0.41 | Contact Map |
| 3i6vA | 1 | 0.9234 | 100 | 0.412 | Contact Map |
| 4kqpA | 1 | 0.9574 | 100 | 0.413 | Contact Map |
| 2ieeA | 2 | 0.9617 | 100 | 0.414 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)