| trial |
| ID: | 1423047387 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 177 (173) | ||
| Sequences: | 5456 (3831.8) | ||
| Seq/Len: | 31.538 | ||
| Nf(neff/√len): | 291.3 |
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: 31.538).
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 |
| 28_E | 72_R | 3.538 | 1.00 |
| 32_Q | 68_L | 3.458 | 1.00 |
| 91_L | 110_V | 2.670 | 1.00 |
| 6_A | 44_T | 2.651 | 1.00 |
| 83_N | 86_L | 2.478 | 1.00 |
| 28_E | 68_L | 2.475 | 1.00 |
| 11_G | 47_Q | 2.453 | 1.00 |
| 52_V | 90_Y | 2.346 | 1.00 |
| 4_D | 42_H | 2.281 | 1.00 |
| 133_P | 149_G | 2.190 | 1.00 |
| 44_T | 58_F | 2.167 | 1.00 |
| 159_D | 162_T | 2.128 | 1.00 |
| 82_T | 115_G | 2.067 | 1.00 |
| 9_L | 27_M | 2.024 | 1.00 |
| 14_K | 115_G | 2.015 | 1.00 |
| 4_D | 108_N | 2.015 | 1.00 |
| 84_T | 112_M | 2.006 | 1.00 |
| 90_Y | 93_D | 1.959 | 1.00 |
| 8_V | 91_L | 1.958 | 1.00 |
| 63_S | 66_D | 1.886 | 1.00 |
| 102_D | 108_N | 1.879 | 1.00 |
| 8_V | 110_V | 1.846 | 1.00 |
| 47_Q | 55_E | 1.778 | 1.00 |
| 133_P | 145_L | 1.777 | 1.00 |
| 109_L | 132_V | 1.742 | 1.00 |
| 10_E | 14_K | 1.708 | 1.00 |
| 20_F | 24_K | 1.694 | 1.00 |
| 142_V | 146_E | 1.676 | 1.00 |
| 14_K | 82_T | 1.638 | 1.00 |
| 56_Y | 67_I | 1.621 | 1.00 |
| 7_F | 27_M | 1.618 | 1.00 |
| 46_L | 87_A | 1.595 | 1.00 |
| 135_G | 145_L | 1.569 | 1.00 |
| 24_K | 71_V | 1.558 | 1.00 |
| 110_V | 131_V | 1.522 | 1.00 |
| 54_V | 90_Y | 1.451 | 1.00 |
| 142_V | 156_L | 1.440 | 1.00 |
| 11_G | 49_S | 1.395 | 0.99 |
| 46_L | 52_V | 1.384 | 0.99 |
| 92_S | 127_G | 1.361 | 0.99 |
| 7_F | 111_Y | 1.356 | 0.99 |
| 52_V | 87_A | 1.354 | 0.99 |
| 11_G | 20_F | 1.349 | 0.99 |
| 46_L | 90_Y | 1.346 | 0.99 |
| 48_Y | 84_T | 1.307 | 0.99 |
| 6_A | 91_L | 1.303 | 0.99 |
| 131_V | 148_I | 1.300 | 0.99 |
| 84_T | 118_A | 1.294 | 0.99 |
| 103_R | 106_A | 1.291 | 0.99 |
| 27_M | 71_V | 1.279 | 0.99 |
| 25_E | 29_E | 1.271 | 0.99 |
| 47_Q | 53_T | 1.265 | 0.99 |
| 82_T | 116_N | 1.262 | 0.99 |
| 141_N | 144_E | 1.255 | 0.99 |
| 88_L | 110_V | 1.254 | 0.99 |
| 21_N | 24_K | 1.253 | 0.99 |
| 88_L | 148_I | 1.242 | 0.98 |
| 8_V | 87_A | 1.217 | 0.98 |
| 69_Q | 73_E | 1.191 | 0.98 |
| 13_D | 79_G | 1.184 | 0.98 |
| 8_V | 46_L | 1.183 | 0.98 |
| 82_T | 114_T | 1.182 | 0.98 |
| 16_G | 76_Y | 1.181 | 0.98 |
| 9_L | 74_I | 1.179 | 0.98 |
| 90_Y | 94_H | 1.173 | 0.98 |
| 54_V | 57_P | 1.172 | 0.98 |
| 135_G | 140_A | 1.167 | 0.97 |
| 6_A | 58_F | 1.166 | 0.97 |
| 29_E | 32_Q | 1.134 | 0.97 |
| 66_D | 69_Q | 1.118 | 0.96 |
| 64_K | 68_L | 1.114 | 0.96 |
| 86_L | 89_R | 1.112 | 0.96 |
| 44_T | 95_S | 1.095 | 0.96 |
| 162_T | 165_R | 1.094 | 0.96 |
| 15_I | 19_D | 1.092 | 0.96 |
| 50_Y | 81_R | 1.092 | 0.96 |
| 143_Q | 147_R | 1.089 | 0.96 |
| 137_G | 140_A | 1.087 | 0.96 |
| 56_Y | 59_S | 1.069 | 0.95 |
| 6_A | 46_L | 1.062 | 0.95 |
| 19_D | 139_N | 1.062 | 0.95 |
| 111_Y | 134_I | 1.058 | 0.95 |
| 117_P | 141_N | 1.055 | 0.95 |
| 31_I | 71_V | 1.054 | 0.95 |
| 35_D | 40_S | 1.047 | 0.94 |
| 113_V | 136_V | 1.039 | 0.94 |
| 4_D | 58_F | 1.032 | 0.94 |
| 118_A | 144_E | 1.023 | 0.93 |
| 56_Y | 70_R | 1.019 | 0.93 |
| 146_E | 150_W | 1.018 | 0.93 |
| 5_V | 109_L | 1.013 | 0.93 |
| 65_G | 69_Q | 1.011 | 0.93 |
| 88_L | 131_V | 1.010 | 0.93 |
| 83_N | 119_S | 1.004 | 0.93 |
| 47_Q | 74_I | 1.000 | 0.92 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3zqkA | 3 | 1 | 100 | 0.167 | Contact Map |
| 4nehA | 1 | 0.9831 | 100 | 0.233 | Contact Map |
| 4cn9A | 2 | 0.9944 | 100 | 0.244 | Contact Map |
| 4okuA | 2 | 0.9209 | 99.9 | 0.25 | Contact Map |
| 4igiA | 1 | 0.9774 | 99.9 | 0.255 | Contact Map |
| 4okrA | 2 | 0.9266 | 99.9 | 0.261 | Contact Map |
| 2b2xA | 2 | 0.9718 | 99.9 | 0.273 | Contact Map |
| 1pt6A | 2 | 0.9831 | 99.9 | 0.276 | Contact Map |
| 1ijbA | 1 | 0.9831 | 99.9 | 0.276 | Contact Map |
| 1mjnA | 1 | 0.9661 | 99.9 | 0.287 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)