| 1DUPA |
| ID: | 1411760267 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 136 (131) | ||
| Sequences: | 1839 (1182.6) | ||
| Seq/Len: | 14.038 | ||
| Nf(neff/√len): | 103.3 |
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: 14.038).
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 |
| 25_T | 28_S | 3.523 | 1.00 |
| 112_Q | 115_E | 2.867 | 1.00 |
| 28_S | 92_D | 2.709 | 1.00 |
| 66_A | 120_M | 2.555 | 1.00 |
| 44_A | 108_S | 2.543 | 1.00 |
| 25_T | 92_D | 2.485 | 1.00 |
| 80_I | 109_F | 2.474 | 1.00 |
| 40_A | 112_Q | 2.398 | 1.00 |
| 9_I | 132_L | 2.383 | 1.00 |
| 30_G | 121_I | 2.344 | 1.00 |
| 31_L | 130_F | 2.337 | 1.00 |
| 27_G | 91_S | 2.295 | 1.00 |
| 48_T | 79_G | 2.241 | 1.00 |
| 76_H | 100_S | 2.152 | 1.00 |
| 69_L | 88_L | 2.067 | 1.00 |
| 44_A | 47_D | 2.055 | 1.00 |
| 5_I | 130_F | 2.039 | 1.00 |
| 78_H | 109_F | 1.962 | 1.00 |
| 23_Y | 127_Q | 1.841 | 1.00 |
| 47_D | 106_Q | 1.828 | 1.00 |
| 59_I | 122_F | 1.826 | 1.00 |
| 52_P | 98_M | 1.726 | 1.00 |
| 45_P | 108_S | 1.725 | 1.00 |
| 58_H | 94_Q | 1.720 | 1.00 |
| 67_M | 88_L | 1.680 | 1.00 |
| 6_D | 131_N | 1.663 | 1.00 |
| 42_E | 110_T | 1.659 | 1.00 |
| 23_Y | 31_L | 1.592 | 1.00 |
| 10_L | 56_A | 1.495 | 1.00 |
| 67_M | 123_V | 1.432 | 1.00 |
| 33_L | 66_A | 1.428 | 1.00 |
| 57_I | 66_A | 1.414 | 1.00 |
| 18_F | 113_P | 1.403 | 0.99 |
| 43_L | 49_T | 1.399 | 0.99 |
| 35_A | 111_I | 1.388 | 0.99 |
| 52_P | 96_Q | 1.358 | 0.99 |
| 54_G | 96_Q | 1.354 | 0.99 |
| 68_M | 120_M | 1.353 | 0.99 |
| 65_A | 88_L | 1.352 | 0.99 |
| 50_L | 98_M | 1.347 | 0.99 |
| 6_D | 58_H | 1.332 | 0.99 |
| 50_L | 76_H | 1.303 | 0.99 |
| 71_R | 116_R | 1.283 | 0.99 |
| 40_A | 113_P | 1.279 | 0.99 |
| 69_L | 123_V | 1.274 | 0.99 |
| 24_A | 34_R | 1.269 | 0.99 |
| 65_A | 69_L | 1.267 | 0.99 |
| 42_E | 108_S | 1.262 | 0.99 |
| 22_T | 34_R | 1.251 | 0.99 |
| 23_Y | 128_A | 1.243 | 0.98 |
| 81_V | 102_W | 1.239 | 0.98 |
| 70_P | 85_L | 1.193 | 0.98 |
| 66_A | 122_F | 1.183 | 0.98 |
| 59_I | 66_A | 1.150 | 0.97 |
| 69_L | 86_V | 1.144 | 0.97 |
| 81_V | 104_R | 1.130 | 0.97 |
| 9_I | 20_L | 1.108 | 0.96 |
| 46_G | 106_Q | 1.092 | 0.96 |
| 94_Q | 136_F | 1.084 | 0.96 |
| 13_R | 113_P | 1.084 | 0.96 |
| 99_I | 118_A | 1.081 | 0.95 |
| 53_T | 99_I | 1.076 | 0.95 |
| 4_K | 129_E | 1.062 | 0.95 |
| 46_G | 105_G | 1.060 | 0.95 |
| 122_F | 128_A | 1.050 | 0.94 |
| 19_P | 34_R | 1.045 | 0.94 |
| 37_L | 113_P | 1.044 | 0.94 |
| 99_I | 117_I | 1.017 | 0.93 |
| 65_A | 123_V | 1.008 | 0.93 |
| 29_A | 65_A | 1.008 | 0.93 |
| 8_K | 135_D | 1.006 | 0.93 |
| 57_I | 97_L | 1.004 | 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 | |
| 1euwA | 1 | 1 | 100 | 0.085 | Contact Map |
| 4gv8A | 6 | 0.9265 | 100 | 0.096 | Contact Map |
| 3zf6A | 1 | 0.9265 | 100 | 0.099 | Contact Map |
| 3tqzA | 1 | 0.9926 | 100 | 0.103 | Contact Map |
| 3hzaA | 1 | 0.9485 | 100 | 0.105 | Contact Map |
| 3mdxA | 1 | 0.9632 | 100 | 0.11 | Contact Map |
| 3c2tA | 2 | 0.9191 | 100 | 0.127 | Contact Map |
| 3f4fA | 3 | 0.9265 | 100 | 0.129 | Contact Map |
| 3ca9A | 2 | 0.9191 | 100 | 0.139 | Contact Map |
| 3p48A | 3 | 0.9265 | 100 | 0.141 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)