| TCF4 distant relatives |
| ID: | 1434655998 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (91) | ||
| Sequences: | 147 (93.3) | ||
| Seq/Len: | 1.615 | ||
| Nf(neff/√len): | 9.8 |
Jackhmmer Results: (2015_01_07)
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: 1.615).
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 |
| 55_Y | 80_E | 2.509 | 1.00 |
| 21_K | 61_R | 1.947 | 0.98 |
| 55_Y | 60_S | 1.841 | 0.97 |
| 47_A | 58_A | 1.737 | 0.95 |
| 21_K | 65_Y | 1.654 | 0.93 |
| 36_K | 55_Y | 1.646 | 0.93 |
| 22_L | 75_I | 1.547 | 0.90 |
| 65_Y | 73_Y | 1.540 | 0.89 |
| 28_P | 52_G | 1.477 | 0.86 |
| 10_V | 69_A | 1.447 | 0.85 |
| 19_V | 47_A | 1.434 | 0.84 |
| 61_R | 77_K | 1.412 | 0.83 |
| 23_V | 43_L | 1.395 | 0.82 |
| 21_K | 43_L | 1.244 | 0.71 |
| 57_S | 85_S | 1.233 | 0.70 |
| 39_R | 61_R | 1.219 | 0.68 |
| 7_H | 10_V | 1.218 | 0.68 |
| 41_E | 55_Y | 1.216 | 0.68 |
| 40_M | 62_D | 1.196 | 0.66 |
| 23_V | 79_L | 1.189 | 0.66 |
| 55_Y | 59_N | 1.178 | 0.64 |
| 50_V | 54_M | 1.171 | 0.64 |
| 8_E | 75_I | 1.169 | 0.64 |
| 41_E | 84_R | 1.166 | 0.63 |
| 13_D | 21_K | 1.165 | 0.63 |
| 37_D | 83_R | 1.162 | 0.63 |
| 39_R | 72_I | 1.158 | 0.63 |
| 19_V | 75_I | 1.151 | 0.62 |
| 54_M | 74_K | 1.148 | 0.62 |
| 19_V | 58_A | 1.142 | 0.61 |
| 30_P | 72_I | 1.110 | 0.58 |
| 8_E | 20_H | 1.103 | 0.57 |
| 18_L | 22_L | 1.099 | 0.57 |
| 20_H | 42_N | 1.098 | 0.56 |
| 41_E | 82_K | 1.085 | 0.55 |
| 59_N | 63_E | 1.085 | 0.55 |
| 23_V | 68_L | 1.081 | 0.55 |
| 14_L | 48_K | 1.080 | 0.55 |
| 37_D | 41_E | 1.075 | 0.54 |
| 27_F | 52_G | 1.070 | 0.53 |
| 17_H | 28_P | 1.046 | 0.51 |
| 49_K | 73_Y | 1.042 | 0.51 |
| 18_L | 65_Y | 1.037 | 0.50 |
| 12_Q | 20_H | 1.030 | 0.49 |
| 60_S | 84_R | 1.029 | 0.49 |
| 88_G | 91_T | 1.015 | 0.48 |
| 81_E | 86_R | 1.013 | 0.47 |
| 44_V | 60_S | 1.013 | 0.47 |
| 18_L | 70_E | 1.007 | 0.47 |
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 | |
| 4i9oA | 1 | 0.7358 | 99.9 | 0.286 | Contact Map |
| 2k0nA | 1 | 0.8019 | 99.7 | 0.53 | Contact Map |
| 2gutA | 1 | 0.6981 | 97.5 | 0.781 | Contact Map |
| 4bk0A | 2 | 0.8019 | 62.5 | 0.892 | Contact Map |
| 4m70E | 4 | 0.7264 | 37 | 0.907 | Contact Map |
| 1j99A | 1 | 0.3396 | 24.7 | 0.915 | Contact Map |
| 2gwhA | 2 | 0.3491 | 23.5 | 0.915 | Contact Map |
| 1q20A | 1 | 0.3396 | 23.4 | 0.916 | Contact Map |
| 1ls6A | 1 | 0.3491 | 23.2 | 0.916 | Contact Map |
| 1aquA | 2 | 0.3396 | 22.8 | 0.916 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)