| Tim23 TMS1and2 My Align |
| ID: | 1488290030 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 70 (70) | ||
| Sequences: | 187 (71.3) | ||
| Seq/Len: | 2.671 | ||
| Nf(neff/√len): | 8.5 |
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: 2.671).
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_P | 32_S | 1.532 | 0.95 |
| 27_N | 40_T | 1.514 | 0.95 |
| 42_L | 46_T | 1.431 | 0.93 |
| 18_F | 22_M | 1.425 | 0.92 |
| 62_S | 65_I | 1.385 | 0.91 |
| 58_I | 61_L | 1.379 | 0.91 |
| 23_Q | 48_R | 1.366 | 0.90 |
| 21_M | 25_L | 1.355 | 0.90 |
| 42_L | 60_A | 1.351 | 0.90 |
| 58_I | 65_I | 1.339 | 0.89 |
| 21_M | 41_V | 1.313 | 0.88 |
| 8_V | 14_G | 1.293 | 0.87 |
| 47_K | 70_I | 1.277 | 0.86 |
| 1_L | 64_N | 1.262 | 0.85 |
| 2_C | 64_N | 1.254 | 0.84 |
| 12_G | 34_G | 1.241 | 0.83 |
| 14_G | 28_I | 1.234 | 0.83 |
| 17_G | 24_G | 1.230 | 0.83 |
| 35_K | 61_L | 1.228 | 0.83 |
| 33_P | 67_N | 1.204 | 0.81 |
| 58_I | 62_S | 1.203 | 0.81 |
| 7_A | 21_M | 1.192 | 0.80 |
| 25_L | 52_L | 1.189 | 0.80 |
| 8_V | 28_I | 1.185 | 0.79 |
| 3_Y | 64_N | 1.153 | 0.77 |
| 4_G | 64_N | 1.140 | 0.76 |
| 14_G | 37_Q | 1.134 | 0.75 |
| 25_L | 37_Q | 1.107 | 0.72 |
| 25_L | 41_V | 1.093 | 0.71 |
| 5_T | 64_N | 1.086 | 0.70 |
| 28_I | 40_T | 1.058 | 0.68 |
| 15_I | 21_M | 1.057 | 0.67 |
| 9_Y | 46_T | 1.046 | 0.66 |
| 15_I | 65_I | 1.037 | 0.65 |
| 19_S | 51_F | 1.034 | 0.65 |
| 2_C | 53_G | 1.030 | 0.64 |
| 37_Q | 47_K | 1.025 | 0.64 |
| 59_L | 66_I | 1.023 | 0.64 |
| 12_G | 59_L | 1.002 | 0.61 |
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 | |
| 1ym5A | 1 | 0.5143 | 2.3 | 0.931 | Contact Map |
| 1xkpC | 1 | 0.4 | 2.1 | 0.933 | Contact Map |
| 2fozA | 1 | 0.6857 | 1.8 | 0.935 | Contact Map |
| 4dunA | 1 | 0.4857 | 1.8 | 0.935 | Contact Map |
| 4v1gA | 3 | 0 | 1.7 | 0.936 | Contact Map |
| 4c9gA | 1 | 0.3714 | 1.6 | 0.937 | Contact Map |
| 2hlyA | 1 | 0.6429 | 1.5 | 0.938 | Contact Map |
| 3o5tA | 1 | 0.7 | 1.4 | 0.939 | Contact Map |
| 3cdwH | 1 | 0.1286 | 1.3 | 0.94 | Contact Map |
| 4ikaD | 1 | 0.2857 | 1.3 | 0.94 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)