| Eelco dam1p 15-115 7-100 |
| ID: | 1481365054 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 94 (87) | ||
| Sequences: | 185 (117.5) | ||
| Seq/Len: | 2.126 | ||
| Nf(neff/√len): | 12.6 |
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: 2.126).
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 |
| 13_L | 16_S | 2.401 | 1.00 |
| 73_S | 81_S | 1.638 | 0.96 |
| 83_A | 88_Q | 1.576 | 0.94 |
| 72_M | 75_S | 1.571 | 0.94 |
| 35_E | 56_S | 1.532 | 0.93 |
| 43_L | 46_N | 1.490 | 0.92 |
| 60_L | 64_L | 1.487 | 0.92 |
| 84_P | 88_Q | 1.444 | 0.90 |
| 46_N | 81_S | 1.442 | 0.90 |
| 33_I | 42_T | 1.399 | 0.88 |
| 84_P | 89_D | 1.394 | 0.88 |
| 31_P | 38_D | 1.389 | 0.87 |
| 25_I | 82_Q | 1.367 | 0.86 |
| 36_L | 50_L | 1.335 | 0.84 |
| 72_M | 79_E | 1.326 | 0.84 |
| 31_P | 66_S | 1.324 | 0.84 |
| 44_D | 48_T | 1.289 | 0.81 |
| 9_D | 13_L | 1.264 | 0.80 |
| 3_S | 8_A | 1.240 | 0.78 |
| 5_M | 9_D | 1.221 | 0.76 |
| 14_T | 17_V | 1.209 | 0.75 |
| 9_D | 15_S | 1.181 | 0.73 |
| 57_L | 74_N | 1.169 | 0.72 |
| 35_E | 38_D | 1.142 | 0.69 |
| 24_T | 50_L | 1.125 | 0.68 |
| 39_S | 80_F | 1.120 | 0.67 |
| 46_N | 69_Y | 1.118 | 0.67 |
| 40_I | 47_F | 1.105 | 0.66 |
| 14_T | 66_S | 1.103 | 0.65 |
| 62_E | 77_C | 1.101 | 0.65 |
| 32_K | 39_S | 1.089 | 0.64 |
| 9_D | 29_L | 1.081 | 0.63 |
| 55_E | 81_S | 1.081 | 0.63 |
| 39_S | 42_T | 1.075 | 0.62 |
| 44_D | 59_D | 1.074 | 0.62 |
| 3_S | 9_D | 1.073 | 0.62 |
| 33_I | 80_F | 1.062 | 0.61 |
| 50_L | 66_S | 1.048 | 0.59 |
| 3_S | 6_K | 1.043 | 0.59 |
| 34_R | 65_G | 1.042 | 0.59 |
| 60_L | 75_S | 1.028 | 0.57 |
| 69_Y | 73_S | 1.026 | 0.57 |
| 12_G | 66_S | 1.023 | 0.57 |
| 42_T | 52_F | 1.023 | 0.57 |
| 41_I | 73_S | 1.022 | 0.57 |
| 43_L | 69_Y | 1.022 | 0.57 |
| 43_L | 79_E | 1.015 | 0.56 |
| 31_P | 57_L | 1.012 | 0.55 |
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 | |
| 1q55A | 4 | 0 | 14.2 | 0.923 | Contact Map |
| 1i7wB | 2 | 0.2766 | 7.5 | 0.932 | Contact Map |
| 4fzsA | 2 | 0.7021 | 5.9 | 0.936 | Contact Map |
| 1ge9A | 1 | 0.5745 | 5.2 | 0.937 | Contact Map |
| 3wpaA | 1 | 0.0851 | 5 | 0.938 | Contact Map |
| 1w99A | 1 | 0.6489 | 4.8 | 0.938 | Contact Map |
| 4d8mA | 1 | 0.7553 | 4.5 | 0.939 | Contact Map |
| 3qxbA | 4 | 0.2979 | 4.1 | 0.94 | Contact Map |
| 2cx6A | 2 | 0.5851 | 4 | 0.941 | Contact Map |
| 4l6rA | 1 | 0.6383 | 3.9 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)