| fox_150_285 |
| ID: | 1415377167 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 140 (117) | ||
| Sequences: | 148 (69.7) | ||
| Seq/Len: | 1.265 | ||
| Nf(neff/√len): | 6.4 |
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: 1.265).
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 |
| 29_I | 68_I | 2.190 | 0.99 |
| 71_S | 74_F | 1.956 | 0.97 |
| 104_F | 107_G | 1.861 | 0.95 |
| 74_F | 97_H | 1.754 | 0.93 |
| 63_R | 74_F | 1.655 | 0.90 |
| 29_I | 42_T | 1.638 | 0.89 |
| 31_M | 77_C | 1.478 | 0.81 |
| 50_I | 83_R | 1.439 | 0.79 |
| 104_F | 111_R | 1.431 | 0.78 |
| 23_Y | 65_Q | 1.409 | 0.77 |
| 57_Y | 83_R | 1.405 | 0.76 |
| 82_A | 88_P | 1.395 | 0.76 |
| 48_Q | 52_D | 1.380 | 0.75 |
| 50_I | 57_Y | 1.378 | 0.74 |
| 76_D | 96_L | 1.363 | 0.73 |
| 11_T | 29_I | 1.355 | 0.73 |
| 63_R | 97_H | 1.349 | 0.72 |
| 79_V | 96_L | 1.337 | 0.71 |
| 92_S | 109_Y | 1.323 | 0.70 |
| 27_S | 74_F | 1.321 | 0.70 |
| 40_M | 63_R | 1.286 | 0.67 |
| 31_M | 54_F | 1.272 | 0.66 |
| 35_Q | 79_V | 1.270 | 0.66 |
| 24_S | 75_N | 1.258 | 0.64 |
| 65_Q | 81_V | 1.256 | 0.64 |
| 56_Y | 68_I | 1.254 | 0.64 |
| 63_R | 73_S | 1.249 | 0.64 |
| 106_N | 114_K | 1.248 | 0.64 |
| 20_K | 26_I | 1.245 | 0.63 |
| 33_I | 39_K | 1.233 | 0.62 |
| 22_P | 54_F | 1.226 | 0.62 |
| 58_R | 98_P | 1.225 | 0.61 |
| 51_M | 57_Y | 1.218 | 0.61 |
| 110_L | 115_R | 1.210 | 0.60 |
| 37_P | 49_W | 1.202 | 0.59 |
| 71_S | 108_C | 1.198 | 0.59 |
| 10_K | 29_I | 1.195 | 0.59 |
| 14_R | 17_P | 1.188 | 0.58 |
| 27_S | 54_F | 1.174 | 0.57 |
| 77_C | 80_K | 1.166 | 0.56 |
| 60_N | 63_R | 1.164 | 0.56 |
| 26_I | 76_D | 1.157 | 0.55 |
| 81_V | 96_L | 1.139 | 0.53 |
| 53_L | 71_S | 1.128 | 0.52 |
| 29_I | 74_F | 1.113 | 0.51 |
| 44_S | 62_Q | 1.111 | 0.50 |
| 50_I | 102_N | 1.109 | 0.50 |
| 11_T | 68_I | 1.109 | 0.50 |
| 45_E | 65_Q | 1.102 | 0.50 |
| 19_A | 73_S | 1.100 | 0.49 |
| 65_Q | 82_A | 1.094 | 0.49 |
| 39_K | 73_S | 1.094 | 0.49 |
| 56_Y | 83_R | 1.088 | 0.48 |
| 57_Y | 92_S | 1.076 | 0.47 |
| 95_T | 103_M | 1.076 | 0.47 |
| 54_F | 103_M | 1.073 | 0.47 |
| 30_T | 110_L | 1.057 | 0.45 |
| 63_R | 110_L | 1.047 | 0.44 |
| 68_I | 74_F | 1.037 | 0.43 |
| 54_F | 77_C | 1.035 | 0.43 |
| 20_K | 58_R | 1.033 | 0.43 |
| 77_C | 104_F | 1.029 | 0.42 |
| 45_E | 97_H | 1.016 | 0.41 |
| 11_T | 14_R | 1.015 | 0.41 |
| 103_M | 106_N | 1.011 | 0.41 |
| 27_S | 71_S | 1.010 | 0.41 |
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 | |
| 1vtnC | 1 | 0.7286 | 100 | 0.31 | Contact Map |
| 2hfhA | 1 | 0.6643 | 100 | 0.335 | Contact Map |
| 2hdcA | 1 | 0.6929 | 100 | 0.335 | Contact Map |
| 1kq8A | 1 | 0.5286 | 100 | 0.344 | Contact Map |
| 2c6yA | 2 | 0.7 | 100 | 0.348 | Contact Map |
| 4lg0A | 1 | 0.6 | 100 | 0.402 | Contact Map |
| 1e17A | 1 | 0.6071 | 100 | 0.407 | Contact Map |
| 2mbfA | 1 | 0.6857 | 100 | 0.414 | Contact Map |
| 3l2cA | 1 | 0.5714 | 100 | 0.424 | Contact Map |
| 3g73A | 2 | 0.6786 | 100 | 0.441 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)