| hes-12 |
| ID: | 1466675212 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 75 (75) | ||
| Sequences: | 80 (54.6) | ||
| Seq/Len: | 1.067 | ||
| Nf(neff/√len): | 6.3 |
HHblits Results: (2016_02)
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: 1.067).
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 |
| 11_R | 38_G | 1.902 | 0.94 |
| 8_A | 56_I | 1.661 | 0.87 |
| 10_H | 45_R | 1.508 | 0.79 |
| 1_L | 4_E | 1.506 | 0.79 |
| 34_M | 40_V | 1.383 | 0.70 |
| 26_F | 31_V | 1.363 | 0.68 |
| 7_P | 10_H | 1.355 | 0.68 |
| 4_E | 38_G | 1.349 | 0.67 |
| 33_E | 40_V | 1.316 | 0.64 |
| 7_P | 45_R | 1.309 | 0.64 |
| 8_A | 39_M | 1.308 | 0.64 |
| 44_A | 55_Y | 1.286 | 0.62 |
| 13_I | 60_V | 1.238 | 0.57 |
| 42_P | 53_L | 1.206 | 0.54 |
| 5_M | 59_K | 1.198 | 0.54 |
| 4_E | 42_P | 1.186 | 0.53 |
| 7_P | 47_P | 1.174 | 0.51 |
| 39_M | 56_I | 1.153 | 0.49 |
| 2_P | 46_R | 1.134 | 0.48 |
| 2_P | 48_S | 1.134 | 0.48 |
| 2_P | 52_D | 1.134 | 0.48 |
| 46_R | 52_D | 1.134 | 0.48 |
| 48_S | 52_D | 1.134 | 0.48 |
| 6_S | 30_R | 1.133 | 0.48 |
| 12_K | 38_G | 1.131 | 0.47 |
| 14_S | 42_P | 1.123 | 0.47 |
| 27_C | 30_R | 1.100 | 0.44 |
| 38_G | 42_P | 1.088 | 0.43 |
| 13_I | 69_R | 1.085 | 0.43 |
| 32_K | 66_A | 1.080 | 0.43 |
| 44_A | 51_S | 1.079 | 0.43 |
| 37_Y | 57_K | 1.078 | 0.42 |
| 16_Q | 58_A | 1.075 | 0.42 |
| 71_K | 74_I | 1.075 | 0.42 |
| 5_M | 36_A | 1.074 | 0.42 |
| 21_F | 67_R | 1.060 | 0.41 |
| 37_Y | 75_Q | 1.043 | 0.39 |
| 1_L | 38_G | 1.043 | 0.39 |
| 54_K | 57_K | 1.043 | 0.39 |
| 22_H | 68_E | 1.041 | 0.39 |
| 19_D | 50_N | 1.040 | 0.39 |
| 5_M | 57_K | 1.032 | 0.38 |
| 26_F | 65_Q | 1.031 | 0.38 |
| 44_A | 61_L | 1.025 | 0.38 |
| 4_E | 36_A | 1.023 | 0.37 |
| 38_G | 41_S | 1.011 | 0.36 |
| 32_K | 35_D | 1.011 | 0.36 |
| 61_L | 65_Q | 1.000 | 0.35 |
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 | |
| 2p23A | 2 | 0.0533 | 3.3 | 0.924 | Contact Map |
| 4geqE | 2 | 0.2533 | 2.7 | 0.927 | Contact Map |
| 1t6uA | 12 | 0.5733 | 2.5 | 0.929 | Contact Map |
| 1wurA | 5 | 0.8933 | 2.5 | 0.929 | Contact Map |
| 2l9sA | 1 | 0.2 | 2.2 | 0.93 | Contact Map |
| 2j5gA | 11 | 0.7733 | 1.9 | 0.933 | Contact Map |
| 3godA | 4 | 1 | 1.8 | 0.934 | Contact Map |
| 1kdxB | 1 | 0.36 | 1.7 | 0.935 | Contact Map |
| 1r44A | 6 | 0.5467 | 1.7 | 0.935 | Contact Map |
| 2lxtC | 1 | 0.44 | 1.5 | 0.937 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)