| glpg |
| ID: | 1493153746 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 181 (177) | ||
| Sequences: | 11886 (8830) | ||
| Seq/Len: | 67.153 | ||
| Nf(neff/√len): | 663.7 |
Jackhmmer Results: (2016_04)
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: 67.153).
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 |
| 52_A | 92_A | 4.910 | 1.00 |
| 91_S | 116_A | 4.399 | 1.00 |
| 44_E | 47_R | 3.407 | 1.00 |
| 94_L | 170_V | 3.245 | 1.00 |
| 56_F | 108_G | 3.148 | 1.00 |
| 51_H | 96_G | 3.138 | 1.00 |
| 119_G | 168_L | 2.532 | 1.00 |
| 15_V | 61_I | 2.508 | 1.00 |
| 92_A | 113_V | 2.425 | 1.00 |
| 98_V | 166_A | 2.414 | 1.00 |
| 99_Q | 160_A | 2.347 | 1.00 |
| 11_M | 65_L | 2.331 | 1.00 |
| 7_T | 84_L | 2.242 | 1.00 |
| 99_Q | 107_F | 1.990 | 1.00 |
| 58_L | 62_L | 1.974 | 1.00 |
| 107_F | 160_A | 1.972 | 1.00 |
| 14_C | 88_T | 1.965 | 1.00 |
| 14_C | 65_L | 1.938 | 1.00 |
| 87_I | 91_S | 1.877 | 1.00 |
| 30_M | 34_A | 1.659 | 1.00 |
| 11_M | 69_W | 1.632 | 1.00 |
| 46_W | 50_T | 1.584 | 1.00 |
| 88_T | 113_V | 1.583 | 1.00 |
| 68_W | 114_V | 1.557 | 1.00 |
| 55_H | 60_H | 1.541 | 1.00 |
| 6_V | 81_S | 1.523 | 1.00 |
| 87_I | 120_Y | 1.517 | 1.00 |
| 18_F | 21_M | 1.514 | 1.00 |
| 123_L | 172_L | 1.469 | 1.00 |
| 7_T | 76_E | 1.464 | 1.00 |
| 36_P | 39_P | 1.450 | 1.00 |
| 28_E | 32_W | 1.449 | 1.00 |
| 40_T | 43_F | 1.431 | 1.00 |
| 15_V | 65_L | 1.405 | 0.99 |
| 66_L | 70_Y | 1.401 | 0.99 |
| 120_Y | 175_A | 1.382 | 0.99 |
| 8_W | 12_I | 1.373 | 0.99 |
| 10_M | 14_C | 1.337 | 0.99 |
| 146_W | 150_G | 1.336 | 0.99 |
| 28_E | 33_L | 1.324 | 0.99 |
| 6_V | 85_I | 1.322 | 0.99 |
| 123_L | 175_A | 1.306 | 0.99 |
| 30_M | 33_L | 1.298 | 0.99 |
| 47_R | 50_T | 1.276 | 0.99 |
| 14_C | 18_F | 1.270 | 0.99 |
| 111_S | 164_H | 1.248 | 0.99 |
| 51_H | 107_F | 1.244 | 0.98 |
| 33_L | 36_P | 1.229 | 0.98 |
| 73_G | 77_K | 1.203 | 0.98 |
| 60_H | 111_S | 1.188 | 0.98 |
| 60_H | 164_H | 1.185 | 0.98 |
| 49_F | 93_L | 1.172 | 0.98 |
| 54_M | 108_G | 1.170 | 0.97 |
| 95_S | 112_G | 1.167 | 0.97 |
| 150_G | 161_N | 1.164 | 0.97 |
| 72_G | 84_L | 1.159 | 0.97 |
| 88_T | 117_L | 1.153 | 0.97 |
| 63_F | 67_W | 1.140 | 0.97 |
| 160_A | 163_A | 1.137 | 0.97 |
| 61_I | 65_L | 1.131 | 0.97 |
| 11_M | 14_C | 1.127 | 0.97 |
| 52_A | 113_V | 1.123 | 0.97 |
| 162_G | 166_A | 1.108 | 0.96 |
| 79_L | 87_I | 1.106 | 0.96 |
| 64_N | 164_H | 1.088 | 0.96 |
| 140_I | 144_L | 1.088 | 0.96 |
| 5_P | 81_S | 1.086 | 0.96 |
| 18_F | 61_I | 1.086 | 0.96 |
| 145_I | 148_V | 1.069 | 0.95 |
| 48_Y | 100_Q | 1.053 | 0.95 |
| 112_G | 163_A | 1.047 | 0.94 |
| 32_W | 35_W | 1.037 | 0.94 |
| 85_I | 89_L | 1.036 | 0.94 |
| 88_T | 110_L | 1.028 | 0.94 |
| 39_P | 42_K | 1.022 | 0.93 |
| 28_E | 31_L | 1.013 | 0.93 |
| 48_Y | 96_G | 1.013 | 0.93 |
| 144_L | 148_V | 1.008 | 0.93 |
| 166_A | 170_V | 1.006 | 0.93 |
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 | |
| 2xovA | 1 | 1 | 100 | 0.154 | Contact Map |
| 4njnA | 1 | 1 | 100 | 0.157 | Contact Map |
| 2nr9A | 1 | 0.9945 | 100 | 0.163 | Contact Map |
| 4qtnA | 3 | 0.326 | 6.4 | 0.933 | Contact Map |
| 4tphA | 2 | 0.9337 | 3.8 | 0.939 | Contact Map |
| 2kluA | 1 | 0.1381 | 3.5 | 0.94 | Contact Map |
| 1pw4A | 1 | 0.9392 | 3.4 | 0.941 | Contact Map |
| 4ldsA | 2 | 0.9061 | 2.4 | 0.946 | Contact Map |
| 2wswA | 1 | 0.9724 | 1.9 | 0.948 | Contact Map |
| 4o9uB | 2 | 0.4088 | 1.9 | 0.948 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)