| Cus-edited |
| ID: | 1419263244 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (99) | ||
| Sequences: | 415 (326.8) | ||
| Seq/Len: | 4.192 | ||
| Nf(neff/√len): | 32.8 |
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: 4.192).
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 |
| 42_H | 72_H | 2.745 | 1.00 |
| 20_I | 98_V | 2.130 | 1.00 |
| 47_D | 72_H | 2.056 | 1.00 |
| 48_I | 72_H | 1.955 | 1.00 |
| 39_V | 79_L | 1.951 | 1.00 |
| 23_A | 101_A | 1.917 | 1.00 |
| 12_L | 25_I | 1.532 | 0.98 |
| 64_Y | 99_L | 1.531 | 0.98 |
| 27_A | 99_L | 1.508 | 0.98 |
| 10_F | 14_T | 1.489 | 0.98 |
| 54_I | 75_Y | 1.468 | 0.97 |
| 22_L | 37_H | 1.435 | 0.97 |
| 42_H | 47_D | 1.434 | 0.97 |
| 43_F | 72_H | 1.416 | 0.97 |
| 28_F | 106_H | 1.400 | 0.96 |
| 67_L | 72_H | 1.397 | 0.96 |
| 41_V | 93_L | 1.384 | 0.96 |
| 39_V | 42_H | 1.370 | 0.96 |
| 19_F | 101_A | 1.343 | 0.95 |
| 72_H | 75_Y | 1.311 | 0.94 |
| 89_V | 93_L | 1.266 | 0.93 |
| 38_S | 46_Q | 1.245 | 0.92 |
| 35_M | 39_V | 1.243 | 0.92 |
| 20_I | 97_I | 1.206 | 0.90 |
| 42_H | 45_E | 1.205 | 0.90 |
| 79_L | 82_K | 1.204 | 0.90 |
| 46_Q | 79_L | 1.202 | 0.90 |
| 53_E | 57_T | 1.189 | 0.89 |
| 26_A | 74_H | 1.158 | 0.87 |
| 17_T | 27_A | 1.155 | 0.87 |
| 16_L | 102_V | 1.148 | 0.87 |
| 20_I | 32_A | 1.138 | 0.86 |
| 48_I | 57_T | 1.132 | 0.86 |
| 46_Q | 83_L | 1.120 | 0.85 |
| 28_F | 82_K | 1.109 | 0.84 |
| 62_L | 105_G | 1.105 | 0.84 |
| 54_I | 60_R | 1.096 | 0.83 |
| 43_F | 75_Y | 1.088 | 0.82 |
| 16_L | 20_I | 1.079 | 0.82 |
| 19_F | 105_G | 1.070 | 0.81 |
| 66_A | 88_S | 1.069 | 0.81 |
| 19_F | 84_I | 1.059 | 0.80 |
| 26_A | 37_H | 1.040 | 0.78 |
| 54_I | 71_F | 1.040 | 0.78 |
| 32_A | 97_I | 1.038 | 0.78 |
| 21_S | 74_H | 1.007 | 0.75 |
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 | |
| 2kseA | 1 | 0.7264 | 98 | 0.64 | Contact Map |
| 2f95B | 1 | 0.5 | 40.1 | 0.858 | Contact Map |
| 3e4oA | 2 | 0.566 | 34.8 | 0.862 | Contact Map |
| 4gycB | 1 | 0.5755 | 16.7 | 0.882 | Contact Map |
| 4bw5A | 4 | 0.8396 | 5.7 | 0.904 | Contact Map |
| 4a01A | 2 | 0.8208 | 5.7 | 0.904 | Contact Map |
| 4i5sA | 2 | 0.1038 | 5.4 | 0.905 | Contact Map |
| 4i9wA | 2 | 0.8491 | 4.2 | 0.91 | Contact Map |
| 4twkA | 2 | 0.8868 | 4.1 | 0.911 | Contact Map |
| 4p02B | 1 | 0.3962 | 2.7 | 0.919 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)