| blast alignment fixed |
| ID: | 1515171797 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 79 (79) | ||
| Sequences: | 1714 (1262.4) | ||
| Seq/Len: | 21.696 | ||
| Nf(neff/√len): | 142.0 |
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: 21.696).
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 |
| 31_V | 50_K | 3.241 | 1.00 |
| 19_K | 22_N | 2.485 | 1.00 |
| 59_E | 79_V | 2.453 | 1.00 |
| 13_A | 29_R | 2.369 | 1.00 |
| 36_Q | 46_T | 2.367 | 1.00 |
| 66_P | 71_K | 2.214 | 1.00 |
| 8_E | 65_K | 2.164 | 1.00 |
| 37_V | 43_Y | 2.112 | 1.00 |
| 34_K | 48_E | 1.979 | 1.00 |
| 66_P | 69_N | 1.972 | 1.00 |
| 44_Y | 62_V | 1.921 | 1.00 |
| 44_Y | 75_E | 1.720 | 1.00 |
| 64_V | 71_K | 1.690 | 1.00 |
| 33_A | 58_Y | 1.572 | 1.00 |
| 44_Y | 64_V | 1.518 | 1.00 |
| 41_T | 66_P | 1.460 | 1.00 |
| 35_E | 47_L | 1.446 | 1.00 |
| 33_A | 50_K | 1.378 | 0.99 |
| 48_E | 60_A | 1.366 | 0.99 |
| 19_K | 74_Q | 1.362 | 0.99 |
| 38_V | 42_M | 1.351 | 0.99 |
| 9_L | 35_E | 1.329 | 0.99 |
| 13_A | 47_L | 1.271 | 0.99 |
| 30_V | 52_G | 1.258 | 0.99 |
| 49_A | 61_K | 1.243 | 0.98 |
| 27_F | 51_D | 1.226 | 0.98 |
| 40_G | 44_Y | 1.205 | 0.98 |
| 14_V | 18_N | 1.196 | 0.98 |
| 74_Q | 77_K | 1.175 | 0.98 |
| 12_F | 65_K | 1.174 | 0.98 |
| 46_T | 60_A | 1.156 | 0.97 |
| 13_A | 17_H | 1.104 | 0.96 |
| 10_A | 14_V | 1.091 | 0.96 |
| 17_H | 21_E | 1.084 | 0.96 |
| 38_V | 44_Y | 1.081 | 0.95 |
| 41_T | 68_E | 1.059 | 0.95 |
| 17_H | 20_K | 1.040 | 0.94 |
| 51_D | 59_E | 1.025 | 0.93 |
| 30_V | 56_K | 1.017 | 0.93 |
| 29_R | 49_A | 1.004 | 0.93 |
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 | |
| 3ul5A | 4 | 0.9747 | 99.6 | 0.067 | Contact Map |
| 2l4vA | 1 | 1 | 99.6 | 0.074 | Contact Map |
| 1eqkA | 1 | 1 | 99.6 | 0.085 | Contact Map |
| 4lziA | 1 | 1 | 99.6 | 0.096 | Contact Map |
| 3imaB | 2 | 0.9367 | 99.5 | 0.108 | Contact Map |
| 5a0oB | 2 | 0 | 99.5 | 0.113 | Contact Map |
| 2kxgA | 1 | 0.962 | 99.5 | 0.124 | Contact Map |
| 4n6tA | 1 | 0.962 | 99.5 | 0.124 | Contact Map |
| 1roaA | 1 | 0.9873 | 99.5 | 0.128 | Contact Map |
| 3gaxA | 2 | 0.9873 | 99.5 | 0.133 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)