| fox_150_285 5-125 |
| ID: | 1415377699 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 121 (110) | ||
| Sequences: | 410 (227.9) | ||
| Seq/Len: | 3.727 | ||
| Nf(neff/√len): | 21.7 |
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: 3.727).
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 |
| 27_M | 50_F | 2.781 | 1.00 |
| 32_A | 37_L | 2.779 | 1.00 |
| 46_I | 53_Y | 2.685 | 1.00 |
| 44_Q | 48_D | 1.939 | 1.00 |
| 67_S | 70_F | 1.880 | 1.00 |
| 100_F | 107_R | 1.839 | 1.00 |
| 71_N | 87_G | 1.656 | 0.99 |
| 25_I | 70_F | 1.619 | 0.98 |
| 22_I | 72_D | 1.509 | 0.97 |
| 77_V | 88_S | 1.506 | 0.97 |
| 25_I | 64_I | 1.495 | 0.97 |
| 106_L | 112_F | 1.467 | 0.97 |
| 23_S | 45_W | 1.401 | 0.95 |
| 100_F | 103_G | 1.351 | 0.94 |
| 64_I | 70_F | 1.344 | 0.94 |
| 73_C | 76_K | 1.334 | 0.93 |
| 104_C | 112_F | 1.332 | 0.93 |
| 16_K | 22_I | 1.331 | 0.93 |
| 19_Y | 50_F | 1.323 | 0.93 |
| 30_Q | 35_K | 1.278 | 0.91 |
| 47_M | 56_N | 1.273 | 0.91 |
| 67_S | 71_N | 1.260 | 0.91 |
| 47_M | 61_Q | 1.254 | 0.90 |
| 52_Y | 56_N | 1.253 | 0.90 |
| 24_L | 28_A | 1.237 | 0.90 |
| 37_L | 41_E | 1.220 | 0.89 |
| 72_D | 93_H | 1.213 | 0.88 |
| 22_I | 85_G | 1.193 | 0.87 |
| 63_S | 68_L | 1.184 | 0.87 |
| 33_P | 49_L | 1.184 | 0.87 |
| 27_M | 73_C | 1.178 | 0.86 |
| 75_V | 94_P | 1.160 | 0.85 |
| 62_N | 69_S | 1.158 | 0.85 |
| 99_M | 107_R | 1.151 | 0.85 |
| 59_R | 70_F | 1.121 | 0.82 |
| 43_Y | 87_G | 1.119 | 0.82 |
| 65_R | 68_L | 1.099 | 0.81 |
| 22_I | 83_K | 1.092 | 0.80 |
| 50_F | 73_C | 1.090 | 0.80 |
| 65_R | 69_S | 1.087 | 0.80 |
| 67_S | 86_K | 1.078 | 0.79 |
| 66_H | 90_W | 1.068 | 0.78 |
| 29_I | 35_K | 1.062 | 0.77 |
| 106_L | 110_K | 1.060 | 0.77 |
| 26_T | 97_G | 1.038 | 0.75 |
| 22_I | 73_C | 1.038 | 0.75 |
| 31_Q | 45_W | 1.031 | 0.74 |
| 29_I | 59_R | 1.028 | 0.74 |
| 60_W | 68_L | 1.022 | 0.73 |
| 71_N | 79_R | 1.021 | 0.73 |
| 59_R | 67_S | 1.021 | 0.73 |
| 74_F | 90_W | 1.004 | 0.72 |
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 | 0.843 | 100 | 0.178 | Contact Map |
| 2hdcA | 1 | 0.8017 | 100 | 0.205 | Contact Map |
| 2hfhA | 1 | 0.7686 | 100 | 0.209 | Contact Map |
| 2c6yA | 2 | 0.8099 | 100 | 0.21 | Contact Map |
| 1kq8A | 1 | 0.6116 | 100 | 0.213 | Contact Map |
| 4lg0A | 1 | 0.6942 | 100 | 0.286 | Contact Map |
| 1e17A | 1 | 0.7025 | 100 | 0.287 | Contact Map |
| 2mbfA | 1 | 0.7934 | 100 | 0.291 | Contact Map |
| 3l2cA | 1 | 0.6612 | 100 | 0.298 | Contact Map |
| 3g73A | 2 | 0.7851 | 100 | 0.308 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)